Right now Ops Manager monitoring identifies MongoDB processes according to hostname:port. Unfortunately, if 2 processes have the same short hostname & port in the same Ops Manager project, they'll be treated the same even if they are actually different processes with different FQDN.

Please either allow the use of additional characteristics (FQDN, replica set name, config server name, etc) for differentiating MongoDB processes or provide some way to tag 2 or more processes so monitoring doesn't accidentally miscategorize them as the same process.